A surgery trainee's guide to writing a manuscript
Tiffany W. Liang, David V. Feliciano, Leonidas G. Koniaris
*
Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
article info
Article history:
Received 31 July 2016
Received in revised form
20 November 2016
Accepted 21 December 2016
Keywords:
Scholarly writing
Surgery training
Writing guide
Academic productivity
Research
Publishing
abstract
Publishing clinical and research work for dissem ination is a critical part of the academic process.
Learning how to write an effective manuscript should be a goal for medical students and residents who
hope to participate in publishing. While there are a number of existing texts that address how to write a
manuscript, there are fewer guides that are specifically targeted towards surgery trainees. This review
aims to direct and hopefully encourage surgery trainees to successfully navigate the process of con-
verting ideas into a publication that ultimately helps understanding and improves the care of patients.
© 2016 Elsevier Inc. All rights reserved.
1. Introduction
One of the core purposes of physicians and surgeons is to
improve human life through the application and advancement of
medical science. This can be done not only by treating patients in
the clinical setting, but also by contributing to the fund of medical
knowledge through innovative research that can lead to improved
future therapies. Innovations in research, however, are not mean-
ingful until they are shared with the general scientific community,
such as through publication.
The objective of this article is to provide surgery trainees with
an overview of how to report to the scien tific literature through
peer-reviewed publications. While there are many p ublished
manuscripts that address paper writing in general, there is less
information that specifically ta rgets the surgery train ee. Those
who would like a more comprehensive guide on this subject are
directed to a book ed ited by Schein and colleagues.
1
Publications
are expected and required for competitive residencies and fel-
lowships, academic jobs, and ultimately promotion and tenure at
academic institutions. While it can be extremely challenging for
surgeons to find the time to perform research, write and suc-
cessfully publish papers, the authors would argue that academic
work in conjunction with direct patient care is essential to a sur-
geon's professional development. While there a re other forms of
academic work (e.g., b ook chapters, presentations at conferences),
the focus here is on writing for publication in peer-reviewed
journals. Fig. 1 serves as a general flowchart guide to the creative
writing process. As many of the points are based upon the empiric
experiences of the authors, the article potentially may present
biases of the authors.
2. Before beginning to write
Before starting the actual writing process, there are certain
preliminary considerations. First, the ideas and data that will be
presented in the manuscript should generally be original and im-
pactful. For research articles, this step should ideally be considered
prior to beginning the data collection process. Recognizing if a
project represents a new direction or a less interesting confirma-
tion of existing ideas is important as one decides if a particular
project is worth pursuing and for what journals it may be appro-
priate. The benefit of investing the time and effort required to
publish a study that represents only confirmatory information
should be carefully considered. Next, determining the type of
article that best presents the finding(s) to the reader will direct its
* Corresponding author. Department of Surgery, Indiana University School of
Medicine, 550 N. University Blvd., UH 1295, Indianapolis, IN 46202, USA.
E-mail addresses: [email protected] (T.W. Liang), [email protected]
(D.V. Feliciano), [email protected] (L.G. Koniaris).
Contents lists available at ScienceDirect
The American Journal of Surgery
journal homepage: www.americanjournalofsurgery.com
http://dx.doi.org/10.1016/j.amjsurg.2016.12.010
0002-9610/© 2016 Elsevier Inc. All rights reserved.
The American Journal of Surgery 214 (2017) 558e563
style and content. Deciding the target journal and authors would
then follow. These steps are essential for building the foundation of
the manuscript and will be described in further detail below.
2.1. Ensure originality and impact of research
If others have already reported what one plans to write, the first
question to answer is what value is there in publishing the same
findings? If there would be considerable value gained in a confir-
matory paper, or if disagreement exists in the literature, this would
support the undertaking of such a project. For example, if one has
the opportunity to report a very large series regarding the treat-
ment of a particular condition with multiple therapies, this
frequently is of broad interest. Reporting complication rates and
potential pitfalls of this condition related to different therapies will
help guide treatment and should be well received. Furthermore,
even if a topic is already discussed in the literature, there may be a
certain aspect of the research that may be novel, providing new
insights. This innovative “angle” of the research should be high-
lighted in the manuscript as well as in the correspondence to the
journal where the manuscript will be submitted.
2.2. Decide on type of article
There are a variety of article types, depending on the type of
information to be conveyed. These include research articles, review
articles, techniques papers, letters to the editor, opinions, case re-
ports or series, and other journal-specific formats, such as a quiz or
interesting image. Each journal has a different profile of article
types that it accepts. Usually this has to do with the scope of the
journal e if its main purpose is to showcase the newest techniques
in vascular surgery (i.e., techniques papers), then it will likely not
accept a manuscript discussing a newly discovered biomarker in
pancreatic cancer (i.e., research article), no matter how significant
the findings are.
Research articles are generally considered the most difficult to
complete, since these require experimentation and/or data collec-
tion and analysis prior to writing. Both basic science and clinical
papers fall into this category. These articles will generally be par-
titioned into introduction, methods, results, and discussion/
conclusion sections. Research articles and clinical reviews remain
the mainstay of surgical journals. These articles are generally
considered the most significant contributions any individual makes
in their academic career.
Review articles are a good way for researchers to analyze the
literature and develop a solid fund of knowledge in an area of in-
terest. The information obtained through this process can often be
used as a foundation for the background when composing related
grants, lectures, theses, and research articles. Reviews will also help
others unfamiliar with the subject get a quick overview of existing
knowledge in that area.
2,3
Techniques papers are used to showcase and describe a pro-
cedure or novel operative approach or, occasionally, an entirely
new type of operation. While a well-written manuscript is a must
for any type of paper, a clear description of how to perform the
particular technique is invaluable in this type of article. Images,
either photographs or well-drawn illustrations, are often better
than text when describing a procedure. As retold by others, “Great
paper, poor art e reject. Poor paper, great art e accept!” The
emphasis in these articles is the technical approach, with a limited
presentation of complications and long-term outcomes. Presenta-
tion format and appropriateness for specific journals should be
considered carefully, as not all journals accept these types of
articles.
Letters to the editor are written in response to an article pub-
lished in a particular journal. They usually question the interpre-
tation of a study or offer an alternative viewpoint. Furthermore,
they can be used to disseminate data and ideas that otherwise
might not be published.
4
Finally, letters to the editor also allow an
opportunity to cite relevant literature that the initial article may not
have sufficiently referenced. Regarding promotion and tenure,
however, many reviewers will not consider letters to the editor as
equivalent to independent research articles. Thus, these articles can
be an excellent adjunct to one's record of scholarly publication but,
like case reports below, should be used judiciously.
Case reports and related article types are written for interesting
and unusual disease presentations, remarkable images that provide
an excellent teaching opportunity, and/or some novel aspect of
management. They can be single-patient reports, a small series of
two or more similar cases, or include a more extensive review of
cases previously reported in the literature.
5
Regardless, case re-
ports, in the authors' experience, can be difficult to publish, as
numerous case reports may have already been written that
encompass what one might think is novel, and reviewers may not
consider the report interesting. Nonetheless, a case report that in-
troduces a new idea that will contribute to better management of
patients is more likely to be accepted.
Rather than considering only a case report as a way to share an
interesting clinical case, there are numerous other article types,
including opinion or editorial-type articles, image reports, and quiz
articles that may be easier to publish and will allow the case to be
presented. These are journal-specific and are not discussed in
further detail here. Nonetheless, the reader is encouraged to review
Fig. 1. How to write an article.
T.W. Liang et al. / The American Journal of Surgery 214 (2017) 558e563 559
different journals and potentially consider these article types to
report their case. Finally, the authors would stress that case reports
and similar manuscripts, although potentially of interest, should
generally not constitute the majority of one's academic produc-
tivity. Authors should try and focus on the other article types that
are more highly regarded.
2.3. Identify the ideal journal(s)
When deciding which journal is best suited for a potential
manuscript, three considerations are the scope, readership, and
scholarly metrics of the journal. The scope of a journal refers to
what types of articles and the topics the journal aims to publish.
Often, the scope is linked to the aims, mission, or purpose of the
journal. The readership is largely determined by the scope and
should be taken into account when choosing a journal in order to
ensure that one reaches the intended audience. Besides ensuring
that the intended type of audience is reached e for example, sur-
geons instead of pediatricians e the size of the audience can be
important as well. Journal citation metrics are one method of
gauging the importance of a journal via a measure of the average
number of times other articles have referenced articles in a specific
journal. Journals with higher citation metrics are generally
considered more prestigious and, therefore, reach a larger audi-
ence. Thus, it is desirable to publish one's article in a journal with a
higher impact factor. The top 20 relevant journals in the surgical
field are listed in order of ranking by impact factor in Table 1,as
reported by the 2014 Journal Citation Reports
®
(Thomson Reuters,
2015). The Eigenfactor score is another method used to rank the
significance of a journal and is also shown in this table. Eigenfactor
is determined by not only taking into account the number of times
a journal is cited by another journal, but also by the influence and
prestige of the citing journal.
6
A good rule of thumb in considering a journal is to determine if it
is indexed by Journal Citation Reports and recognized by the United
States National Library of Medicine and National Institutes of
Health shared website, PubMed commons (http://www.ncbi.nlm.
nih.gov/pubmed). Another factor suggestive of quality is if a jour-
nal is supported by a scientific, medical or surgical society. While it
may be more difficult to publish a manuscript in one of these peer-
reviewed or refereed journals that are listed on PubMed and the
Journal Citation Reports, the end result of the peer-review process
in these journals will likely be a better paper that will be accessed
more by other researchers.
Many new journals will not be listed by PubMed or have a
Journal Citation Report listing, as a journal must be out for at least a
few years to generate such metrics. The Journal Citation Report
provides metrics for approximately 11,700 journals. Thus, there
arguably is not a need to publish in unlisted journals unless a
particular project has been rejected from a number of journals
listed. In some instances, the term “predatory journal” has been
introduced for unlisted journals that have little or no peer-review
process, are not indexed in these databases, and may offer publi-
cation for a fee. Publishing in such journals may prevent wide-
spread dissemination of the manuscript and, therefore, fail to
promote the goals of academic work.
7
2.4. An algorithm for choosing appropriate journals
How does one go about finding the right journal? Considering a
top journal, such as listed in Table 1, would certainly be a good first
choice. Another efficient method to search for a suitable journal is
through search engine sites. A sample of such sites that are free of
charge to the general public can be found in Table 2. These search
engines are also good for identifying multiple candidate journals, in
case one's first choice does not pan out. The journals identified by
these sites, however, should always be further investigated to
ensure suitability for the manuscript being submitted. Another
caution is that some journal finder sites are geared only to journals
affiliated with a particular publishing company. Therefore, their
search results may not represent all possible relevant journals. In
any case, consulting with a mentor and/or senior author is usually
warranted for novice researchers. The authors' bias is also to use
only journals that are referenced by Journal Citation Reports
®
(Thomson Reuters), which allows sorting of journals by topic and
impact factor.
2.5. Identifying the author(s)
Authorship is important to determine early in the writing pro-
cess, and it is suggested to be inclusive.
8
The senior author should
ultimately be responsible for who the authors are and the order in
which their names are listed. If there is no senior author, then all
co-authors should come to an agreement on the final decision. The
Table 1
Top 20 surgical journals ranked by impact factor (2014 Journal Citation Reports
®
, Thomson Reuters, 2015).
Rank Journal Total cites Impact factor Eigenfactor score
1 Annals of Surgery 41,468 8.327 0.07481
2 Journal of Neurology Neurosurgery and Psychiatry 25,650 6.807 0.03499
3 Journal of Heart and Lung Transplantation 8562 6.650 0.02437
4 American Journal of Transplantation 18,092 5.683 0.05320
5 British Journal of Surgery 20,540 5.542 0.03445
6 Journal of Bone and Joint Surgery e American Volume 37,434 5.280 0.04747
7 American Journal of Surgical Pathology 18,910 5.145 0.03022
8 Journal of the American College of Surgeons 13,352 5.122 0.03631
9 Endoscopy 8546 5.053 0.01610
10 Archives of Surgery 13,280 4.926 0.01880
11 Liver Transplantation 9357 4.241 0.01762
12 Journal of Thoracic and Cardiovascular Surgery 23,757 4.168 0.05431
13 Surgery for Obesity and Related Diseases 3158 4.066 0.00940
14 JAMA Surgery 785 3.936 0.00371
15 Annals of Surgical Oncology 19,490 3.930 0.05779
16 Annals of Thoracic Surgery 32,052 3.849 0.06305
17 Transplantation 24,021 3.828 0.03823
18 Diseases of the Colon & Rectum 13,256 3.749 0.01911
19 Obesity Surgery 9098 3.747 0.01661
20 Journal of Neurosurgery 29,516 3.737 0.03310
T.W. Liang et al. / The American Journal of Surgery 214 (2017) 558e563560
first author(s) typically earns the title by contributing the most
effort into developing the project, performing the data collection
and analysis process, and/or writing the manuscript. The senior
author, if different from the first author, is usually the person who
takes responsibility for the paper overall and might be the mentor
for the more junior first author. The corresponding author is
responsible for communicating with the journal as well as with
readers with questions or comments after publication. The senior
and corresponding authors are often the same person. All authors
should agree on the order of middle authors, which may be
determined by order of contribution. A potentially useful scoring
system to determine order of authorship has been proposed by
Petroianu.
9
It involves more heavily weighted criteria such as cre-
ation of the original idea and method as well as less heavily
weighted items such as study funding and provision of materials.
9
Authorship can be a difficult issue. Familiarity with criteria for
authorship is suggested and reviewed by the International Com-
mittee of Medical Journal Editors. Briefly, according to this com-
mittee, meeting the criteria for authorship requires that all authors
have made considerable contributions to the following
1
: the
conception and design of the work or to the collection, analysis, and
interpretation of the generated data
2
; writing the manuscript or
critically reviewing and revising it for intellectual content; and
3
approving the final version of the manuscript for publication.
10
Some journals will require a description of each author's contri-
butions. Any individual who does not meet all the criteria, but has
contributed to the work, could alternatively be acknowledged at
the end of the article.
10
Simply having contributed cases or funding
to a study, or providing materials or reagents for an experiment
generally is considered insufficient to warrant authorship.
3. Writing
Composing and refining the manuscript can be an intimidating
undertaking, especially for the novice author. Over time, the pro-
cess becomes easier. Initially, it is useful to focus one's thoughts and
to approach writing the paper in manageable sections. The stan-
dardized format for research articles is discussed below in section
titled “Parts of the Paper,” as well as general guidelines for article
sections. Finally, a review by a professional editor may be worth-
while to ensure that the information is presented in the most un-
derstandable way.
3.1. Focus your thoughts
It is essential to discuss and critically review data and ideas with
co-authors and mentors. The paper's main point and how the
findings and paper will impact the field of interest should be
identified so that this might be more clearly conveyed in the
manuscript. Authors should consider what to present and keep
focused on a particular topic. Separating a paper with too broad of a
scope into two or more focused papers should be considered.
Similarly, authors should be clear regarding the type of article they
are targeting; for example, authors should avoid combining a
research article with a techniques or review paper.
3.2. Parts of the paper
Most papers have abstracts at the beginning that convey the
main points of the article. The abstract structure may differ by
journal and article type. For structured articles presenting original
Table 2
Journal search engines.
Search engine Website(s) Input options Output
Edanz journal selector http://www.edanzediting.com/journal_selector General
information
Journal name
Publisher
Field of study
Abstract, keywords
Journal name
Scope and related information
Publisher
Impact factor
Frequency
Open access
Elsevier journal finder http://journalfinder.elsevier.com/ Title
Abstract
Fields of research
Open access filter
Journal name
Confidence of match
Impact factor
Open access, fee
Editorial time
Acceptance rate
Production time
Embargo period
Scope and related information
Journal/author name estimator (JANE) http://biosemantics.org/jane/index.php Title
Abstract
Keywords
Language
Publication type
Open access options
PubMed Central
filter
Confidence of match
Journal name
Open access
Article Influence score
Similar articles
Springer/BioMed central/Chemistry central journal
selector
http://www.springeropen.com/authors/authorfaq/
findout
http://www.biomedcentral.com/authors/authorfaq/
findout
http://www.chemistrycentral.com/authors/authorfaq/
findout
Abstract
Impact factor filter
Open access filter
Confidence of match
Journal name
Impact factor
Frequency
Publishing model (e.g. open
access)
Web of science™ Journal Citation Reports
®
http://about.jcr.incites.thomsonreuters.com/ Journal category
Impact factor range
Publisher
JCR year
Open access filter
Journal name
Total cites
Impact factor
Eigenfactor score
JCR, Journal Citation Reports.
T.W. Liang et al. / The American Journal of Surgery 214 (2017) 558e563 561
research, the abstract is generally composed of four sections:
background and objectives, methods, results, and conclusions. Such
distinct sections may not be appropriate for reviews or case re-
ports; rather, a summary is adequate in these types of articles.
Research articles tend to follow the traditional introduction,
methods, results, and discussion/conclusion sections format,
otherwise known as “IMRAD.
11e18
” Other article types may not
follow the typical IMRAD format, but usually have introduction,
body, and discussion/conclusion sections. Generally, the introduc-
tion consists of a few paragraphs that briefly describe the back-
ground of the project and why the paper is written. All manuscripts
should ideally include how the work is novel and/or how it hopes to
impact patient care. The methods section describes the approach of
the project and how the data collection and analyses were per-
formed, as well as details of any relevant procedures and materials.
The results section describes the information that is generated from
data collection and analyses and may include the initial interpre-
tation of this information. The discussion section consolidates the
project's findings and interpretations of its results, and it might
include suggestions on how these findings can impact patient care.
The conclusion section should also discuss how the study findings
should be incorporated into models of current understanding as
well as discuss limitations around the interpretation of the data
presented. Future directions of research are also generally included
in this section. Finally, the discussion might end with a take-home
message.
Most scholarly articles reference other publications and, there-
fore, will have a reference or bibliography section at the end. The
number of references and its citation style will be dictated by the
journal that the article will be submitted to. Using a reference
manager (i.e., a software program that automates organization of
citations) is helpful, as it can usually automatically format the ref-
erences to journal-specific requirements. This feature is especially
useful when resubmitting the same article to a different journal.
Additional items include tables and figures that are referenced
in the manuscript or supplementary material (usually additional
figures and tables, or miscellaneous methods that further clarify
those mentioned in the main text) that could not be included in the
main article. Authors can always consider hiring a professional ar-
tist or using computer software to generate informative, profes-
sional appearing illustrations. All photos should be of high quality.
It is worth mentioning that the order of writing may not follow
the order in which the sections of the paper were described above.
It might make more sense to start with writing the methods and
results, then move on to the introduction and discussion, possibly
after discussions with co-authors and others regarding the study's
significance. Completion of the abstract may be considered once all
the sections are relatively finalized. Alternatively, the abstract may
actually be the first item that one writes as it will then serve as a
guide for the rest of the paper, especially if submitting an abstract to
a conference prior to the actual writing of the manuscript.
4. Ethics of writing
As with all academic endeavors, one should abide by a basic
code of ethics when writing a manuscript. Most would agree that
plagiarism, or reproducing others' work (their ideas even more so
than merely their words
19
) as your own, is a blatant violation of
ethical conduct.
Self-plagiarism, however, appears to be less commonly defined
and is often misunderstood. Having more than 30% of two or more
of your own published works matching in text is one useful defi-
nition of self-plagiarism.
20
This concept, however, also involves
more nuanced characterizations. Mohapatra and Samal have sug-
gested that there are 3 types of self-plagiarism
1
: publishing two (or
more) manuscripts that have the same data but with different
words
2
; splitting up one larger study into separate publications in
order to increase the number of publications, even though the larger
study would make more sense or better support the findings (i.e.,
“salami publications”); and
3
using text from one's own previously
published work in a new work.
21
To further clarify the second point,
the key is whether the intent is merely to obtain more publications
or if it is to improve the paper. For example, the authors of this
manuscript would argue that dividing up a manuscript because a
topic is too broad is not an example of ethical misconduct, since a
large combined manuscript would add unnecessary confusion to
the reader and does not add value to the results. In any case,
deception is the distinguishing factor of self-plagiarism,
20,22
as it is
for any form of plagiarism.
In order to screen for possible cases of plagiarism, many journals
use software services such as iThenticate (http://www.ithenticate.
com/). For a fee, authors themselves can also access this service,
as it is useful to check even for unintentional plagiarism or self-
plagiarism.
Dealing with a conflict of interest is a separate ethical issue. As
one section editor of the Journal of Investigative Dermatology wrote
in an editorial, it is defined as having “a set of conditions [that] is
operating that could have a marked influence on behavior.
23
”
Having a conflict of interest by itself is not necessarily problematic,
but rather it is the failure to disclose that has ethical implica-
tions.
15,23
Transparency, disclosure, and peer review are good ways
to address conflicts of interest, whether financial or personal in
nature.
24
Lastly, the topic of self-citation should be mentioned. It is
certainly acceptable and even required when referring to previous
relevant work (to avoid deception in self-plagiarism), but authors
should exercise restraint. This practice can artificially give the
appearance of increased academic productivity and, therefore, be
an ethical dilemma. Moreover, excess self-citations may not be well
received by reviewers and are improper if the citation of work of
others may be more appropriate.
5. Conclusion
Everyone from students to senior surgeons should advance their
personal and professional development as well as the field of sci-
ence and medicine at large. Even if a trainee decides not to be
involved in research in the future, at least he or she is familiar with
the process of writing and has the ability to more critically assess
the scientific literature. It can be argued that it makes one a better
physician and surgeon over time.
Conflicts of interest
None.
Funding sources
This research did not receive any specific grant from funding
agencies in the public, commercial, or not-for-profit sectors.
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